DNA Duplex Formation with a Coarse-Grained

Article pubs.acs.org/JCTC

DNA Duplex Formation with a Coarse-Grained Model Maciej Maciejczyk,†,‡ Aleksandar Spasic,†,§ Adam Liwo,†,∥ and Harold A. Scheraga*,† †

Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14850, United States Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury, 11-041 Olsztyn, Poland § Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, United States ∥ Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland ‡

S Supporting Information *

ABSTRACT: A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem. 2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole−multipole Debye− Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

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INTRODUCTION DNA is a blueprint of life. Since Watson and Crick proposed its three-dimensional structure,1 much effort has been spent to understand its structure and dynamics. Formation of the Watson−Crick double-helix from separated strands is a biologically very important process observed during replication, translation, or DNA repair. It has been the subject of many experimental biochemical and biophysical studies. Also, recently, the rapidly growing field of computer simulations of biological systems has developed models and tools that can provide some insight into this important process. All-atom molecular dynamics (MD) methods offer the deepest insight into the time evolution of DNA at the atomic level. The CHARMM2 and AMBER3 simulation packages have been used to study the duplex dynamics of DNA, mainly in the vicinity of equilibrium. The highlights of near-equilibrium allatom DNA molecular dynamics simulations include the systematic study of nearest-neighbor effects on various short DNA sequences performed by the Ascona B-DNA Consortium,4 and the microsecond simulations of the DrewDickerson dodecamer5 or the κB DNA element.6 Although allatom MD simulations have proven to be very useful for studying near-equilibrium dynamics, their very high computational cost, related to the large number of degrees of freedom and high-frequency oscillations, forcing a short time-step of integration, currently render them unsuitable for simulating long time-scale nonequilibrium processes, such as formation of duplex DNA from separate strands. Only recently, those enhanced sampling methods, such as replica exchange,7 © 2014 American Chemical Society

facilitated simulations of formation of very short (4 base pair (bp)) duplexes of DNA.8 The combination of metadynamics9 and replica exchange, called BE-META method,10 was applied to slightly larger system, DNA hexamer,11 but the moreimportant biological process of formation of long helices remains prohibitively expensive for all-atom MD simulations and has recently become a target for coarse-graining methodology. Coarse-grained models can be divided into three categories: statistical models, continuum models, and reduced interactioncenter models. In the first category, the early work of Zimm and Rice12 and Poland and Scheraga13 neglected all structural and dynamical information and used only the free-energy gain per base-pair formation for computation of the partition function, which, in turn, was transformed into a thermodynamic picture of the process of helix formation. The continuum models approximate dsDNA as a continuum elastic rod and by design cannot be applied to the DNA formation process.14−16 The last category covers all models in which groups of atoms are replaced by a reduced number of interaction centers connected by elastic and/or rigid virtual bonds.17−45 A properly designed coarse-graining procedure should reduce the number of interaction centers, leading to a significant speedup of computations, but simultaneously, the simplified potential energy function should include the most important interactions that determine the behavior of the real system. There are two Received: July 27, 2013 Published: September 22, 2014 5020

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Figure 1. Coarse-grained representation of fragments of the DNA chain superimposed on the atomic representation. Four basic building blocks A, T, G, C attached to small fragments of backbones are shown. Charged beads, which replace phosphate groups, are marked red; neutral beads, which replace deoxyriboses, are marked dark blue. Dipolar beads have different colors for different bases: A, pink; G, green; T, cyan; and C, yellow. Dipolar beads symbols are defined for all building blocks. The internal degrees of freedom used for the definition of the bonded part of the potential energy function (eq 2) are defined in Tables 1−4. For clarity, symbols of beads used for definition of bonded potentials of the backbone are shown for thymine only. The longer fragment of coarse-grained strand of DNA with ATGC sequence overlapped on the atomic model is shown in the right panel. Sequential numbers of consecutive building blocks are assigned.

position in the polynucleotide chain but rather depends on their relative position and orientation in space. The third model named NARES-2P, which does not incorporate any Go̅-like potentials and successfully folds double-stranded DNA from separate strands was recently published by our group.43 NARES-2P model was developed in parallel to the rigid-body model presented in this paper. NARES-2P is a lower-resolution model with two interaction centers per nucleotide (located on phosphate groups and bases), and it seems to be a minimal physics-based model capable of folding of a double-helix from separate strands. The rigid-body model presented here has more interaction centers and more internal degrees of freedom than NARES-2P, and consequently, it is computationally more demanding. Although the conformational space of rigid-body model is larger than in case of NARES-2P, it is still capable of locating double-helical structures in simulated annealing process started from separate strands. The advantage of the dipolar-bead model over recently published NARES-2P is its higher resolution. Another model, which is capable of folding dsDNA from separate strands, was published recently by Cragnolini et al.45 The degree of coarse-graining (6−7 interaction sites per nucleotide) is similar to that of our dipolar-bead model. However, as opposed to our dipolar-bead model, which places more emphasis on the representation of nucleic-acid bases, the model of Cragnolini et al. elaborates on the nucleotide backbone, which is represented by 5 sites per nucleotide than on the nucleic-acid bases, which are represented by 1 or 2 interaction sites, depending on the kind of base; it also utilizes a classical bonded potential and a many-body nonbonded potential responsible for correct Watson−Crick hydrogenbonding and was parametrized in a “top-down” fashion. This

common approaches to the problem of parametrization of a coarse-grained model.37 In the “top-down” parametrization method, selected parameters are adjusted to reproduce largescale properties of the investigated systems. In the “bottom-up” parametrization method, interactions are directly determined from either all-atom molecular dynamics simulations or quantum chemistry computations applied to some model systems. In the past decade, many coarse-grained models of DNA have been developed, but only several of them managed to form double-stranded DNA from separated complementary chains. A three-bead-per-nucleotide model of de Pablo and coworkers27 was successfully used to study DNA melting30 and the renaturation processes.31 The model was designed around the potential energy function, which effectively depends on the single parameter ϵ, which was optimized to reproduce experimental melting curves. The base−base interactions were approximated by a Go̅-like potential.46 The model of Ouldridge et al.37 successfully addresses the phenomena of single-strand stacking, duplex hybridization, and DNA hairpin formation processes. The model was also applied to study DNA Holliday junctions self-assembly32 and DNA nanotweezers.36 Although both models successfully fold double-stranded DNA from separate complementary chains, they rely on base−base nonbonded potentials, which either distinguish between native and non-native pairs27 or nearestneighbors and all remaining pairs.32 Such an approach should speed up the in silico folding process, because many “unwanted” free energy local minima are eliminated, but in the real physical system, the nonbonded potential energy of two interacting bases does not depend on their sequential 5021

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model does not incorporate any Go̅-like potentials and does not treat the interactions between nearest-neighbor nucleotides differently than those between the other pairs of nucleotides. In this paper, we present a physics-based, middle-resolution model of DNA, which is capable of folding the double-helical structure from separate complementary strands. The model was parametrized in the “bottom-up“ fashion, although some adjustment of parameters was necessary to obtain correct balance of key interactions. The non-bonded pairwise potentials do not depend on the sequential position of interacting bases in the polynucleotide chain because the native and non-native, nearest-neighbors, and all other pairs rely on the same potential energy function, which includes a LennardJones and an electrostatic term. The full, physics-based (PB model) version of model keeps stable canonical B DNA double helices in a long room-temperature simulations and folds short DNA molecules. The reduced version of the model, in which base−base intrastrand interactions are limited to nearest neighbors (NN model), successfully folds canonical B DNA from separate complementary strands for all tested systems.

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METHODS The Model. The coarse-grained model of DNA is built of three types of particles: • neutral bead, uncharged Lennard-Jones sphere, • charged bead, Lennard-Jones sphere with an electric charge located in its center, • dipolar bead, Lennard-Jones sphere with an electric dipole located in its center. The DNA chain is built of six types of chemical units: phosphate group (P), deoxyribose (S), adenine (A), thymine (T), guanine (G), and cytosine (C). In the coarse-grained approximation, atoms that constitute each unit are replaced by the three types of beads defined above. The deoxyribose ring is replaced by one neutral bead, the phosphate group is replaced by one charged bead and each base is replaced by a set of dipolar beads. The distances between the dipolar beads of each base are fixed.47 A schematic representation of the coarsegrained units overlapped on their atomic representation is shown in Figure 1. The parametrization of the bead model is described in the Parametrization section. Each chemical unit in the coarse-grained approximation constitutes a rigid body. The origin of the local coordinate frame of each rigid body is located at its center of mass, and its axes are aligned with the principal axes of the moment of inertia tensor. The position and orientation of each rigid body with respect to the global coordinate frame is described by a vector− tensor pair (R,Q), where R is the position of the center of mass and Q is the rotation matrix. In the model, two types of rigid bodies can be distinguishedspherical (P and S) and planar (A,T,G,C). The spherical rigid bodies interact with other particles only by central forces (see “Potential Energy Function”), and their orientation is irrelevant; therefore, a constant rotation matrix Qsphere = const is assigned to them. The orientation of each planar rigid body is described by a 3 × 2 rotation matrix Qplanar and varies as the rigid body changes its orientation during a simulation run. The geometry of the chain is defined in vector−tensor space (Ri,Qi) where i = 1,...,N and N is the number of rigid bodies. The relations between global coordinates (Ri, Qi) and distances between various beads, used for definitions of nonbonded interactions, are shown in Figure 2.

Figure 2. Relations between global coordinates (R,Q) and distances between beads for interactions of (a) two spherical rigid-bodies, where there is only one distance rij = |Rij|; (b) spherical and planar rigid body, where distances between interacting beads are functions of global coordinates given by eq 9; and (c) two planar rigid-bodies, where distances between interacting beads are given by eq 13.

Rigid bodies are connected by elastic virtual bonds and form a nucleic acid chain as shown in Figure 1. Three rigid bodies connected by two virtual bonds form a virtual-bond angle and four rigid bodies connected by three virtual bonds form a virtual-bond dihedral angle. All virtual bonds, virtual-bond angles, and virtual-bond dihedral angles are listed in Tables 1, 2, and 3, respectively. Equations of Motion. The algorithm of Leimkuhler and Reich,48 which is based on the RATTLE49 constraint method applied to rotation matrices, was used for the description of rotation of rigid bodies. A slightly different version of this Table 1. Definitions of Virtual Bonds and Parameters of the Bonded Part of the Potential Energy Functiona

a

5022

virtual bond

kd (kcal/(mol Å2))

d0 (Å)

P5−S P3−S S−B(Pur) S−B(Pyr)

12.45 25.85 26.55 54.23

3.86 3.58 4.82 4.20

For definition of symbols see Figure 1. dx.doi.org/10.1021/ct4006689 | J. Chem. Theory Comput. 2014, 10, 5020−5035

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2P models, we do not average over any degrees of freedom of the nucleic-acid bases, the interactions between which are highly directional. In the UNRES model, we did average over the angles of rotation (λ) of the peptide groups about the Cα...Cα axes; hence, the multibody terms in the UNRES force field are important.52 In our highly reduced NARES-2P model of nucleic acids,43 averaging is carried out over the rotation of nucleic bases about their long axes. The potential energy function of the system is a sum of the bonded and nonbonded parts:

Table 2. Definitions of the Virtual-Bond Angles and the Parameters of the Bonded Part of the Potential Energy Functiona virtual-bond angle

kα (kcal/(mol·rad2))

α0 (rad)

P5−S−P3 S5−P5−S P5−S−B(Pur) P5−S−B(Pyr) P3−S−B(Pur) P3−S−B(Pyr) S−B−X(Ade) S−B−Y(Ade) S−B−X(Thy) S−B−Y(Thy) S−B−X(Gua) S−B−Y(Gua) S−B−X(Cyt) S−B−Y(Cyt)

10.69 7.59 7.02 8.68 10.47 13.18 32.87 32.87 42.82 42.82 31.61 31.61 43.95 43.95

2.11 1.66 1.83 1.62 1.90 2.00 2.71 1.97 1.10 2.64 2.22 0.67 2.31 2.38

U (R, Q) = Ubonded + Unonbond

(1)

Although both the bonded and nonbonded parts depend on the Cartesian-rigid-body degrees of freedom (R,Q), it is more convenient to define the former as a function of the internal degrees of freedom defined in Tables 1−4 (the internal degrees Table 4. Definitions of the Virtual-Bond Improper Dihedral Angles and the Parameters of the Bonded Part of the Potential Energy Functiona

a

S−B−X and S−B−Y are virtual-bond angles between the S−B virtual bond and the X and Y axes of the moment of inertia tensor of a rigid body. (cf. Figure 1)

algorithm, based on the SHAKE50 (rather than the RATTLE) constraint method, showed superior stability51 compared to the other commonly used quaternion-based integration scheme. However, this algorithm (based on SHAKE) was not implemented in our work. The time-evolution of the system is defined in the vectortensor phase space (Ri, pi, Qi, Pi), where pi and Pi are the linear momentum and generalized angular momentum of the i-th particle, respectively. For a planar rigid body, the rotation matrix is a 3 × 2 tensor, subject to the orthogonality condition QT·Q = I2, where I2 is a 2 × 2 unit diagonal matrix. The leapfrog (Verlet) algorithm was used for propagation of translations, and the R-RATTLE (rotational RATTLE) discretization scheme was applied to the rigid-body rotations.48 Potential Energy Function. As in our UNRES model of polypeptide chains developed earlier,52 the effective energy function of our nucleic-acid model stems from the potential of mean force (PMF) of polynucleotide systems immersed in water. The PMF is then to be expanded into a cluster-cumulant series, which, in general, gives rise to the neo-classical local and two-body and nonclassical multibody terms.52 However, because we keep more explicit degrees of freedom than in the UNRES model, the multibody terms do not seem to be necessary. In particular, in contrast to the UNRES and NARES-

a

virtual-bond improper dihedral angle

kγ (kcal/(mol·rad2))

γ0 (rad)

P5−P3−S−B(Pur) P5−P3−S−B(Pyr)

7.74 7.74

2.10 1.90

cf. Figure 1.

of freedom are functions of the (R,Q) vector). The bonded part has a commonly used form Ubonded = Ubond + Ubondangle + Udihedralangle + Uimproper (2)

where: Nbonds

∑

Ubond =

kd(di − di0)2

(3a)

i

Nangles

Ubondangle =

kα(αi − αi0)2

∑

(3b)

i Ndihedrals

4

∑ ∑ Ci ,ncos(nθi) + Di ,nsin(nθi)

Udihedralangle =

i

(3c)

n=0

Nimproper

Uimproper =

∑

k γ(γi − γi0)2

(3d)

i

Table 3. Definitions of the Virtual-Bond Dihedral-Angle Parameters of the Bonded Part of the Potential Energy Functiona,b virtual-bond dihedral angle

C0

C1

C2

C3

C4

D1

D2

D3

D4

P5−S−P3−S3 S5−P5−S−P3 S5−P5−S−B (Pur) S5−P5−S−B (Pyr) S3−P3−S−B (Pur) S3−P3−S-B (Pyr) P5−S−B−X (Ade) P5−S−B−X (Thy) P5−S−B−X (Gua) P5−S−B−X (Cyt)

0.553 0.985 1.168 1.246 0.478 0.706 3.500 3.500 3.500 3.500

−0.340 0.422 −0.772 −0.403 0.098 −0.069 3.202 3.499 −3.497 −3.497

0.453 −0.485 −0.310 −0.212 0.126 0.316

0.001 −0.002 −0.008 0.095 −0.043 −0.151

−0.044 −0.053 0.023 0.082 −0.028 −0.125

0.102 −0.230 0.530 −0.092 0.251 −0.201 1.412 0.731 0.650 0.153

−0.240 −0.343 −0.380 −0.661 0.202 −0.085

0.090 −0.084 0.150 −0.038 −0.045 0.043

−0.145 −0.057 −0.245 −0.067 −0.033 −0.049

a

P5−S−B−X virtual-bond dihedral angle describes rotation of the base around the S−B pseudoglycosydic bond. bcf. Figure 1. All parameters in kcal/mol. 5023

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the k-th dipolar bead of the j-th base. It should be noted that rkij distances are functions of the distance Rij between the sugar and the base and the orientation Qj of the base (see Figure 2).

Both bond-stretching and angle-bending terms are approximated by harmonic potentials. kd and di0 are harmonic force constants and equilibrium distances for bond stretching interactions; kα and αi0 are harmonic force constants and equilibrium angles for the bond-angle bending potential. The general form of the dihedral-angle torsion potentials is a fourthorder Fourier series, although such a long expansion was used only for the backbone dihedral angles (see details in the Parametrization section). Ci,n and Di,n are fourth-order Fourier expansion coefficients. The torsional terms are the only higher (second52) order terms that are present in the energy function; however, they still belong to the neo-classical term set. The harmonic Uimproper potential was introduced to maintain the correct position of the center of mass of the base with respect to the sugar ring and surrounding phosphate groups. kγ and γi0 are harmonic force constant and equilibrium values of the improper dihedral angles. For a detailed geometric definition of the internal degrees of freedom related to the bonded potentials see Figure 1 and Tables 1−4. The force constants and equilibrium positions were determined by fitting the analytical expressions to the potentials of mean force for model systems. The procedure is described in the Parametrization section. The nonbonded energy is a sum of van der Waals and electrostatic energies and is given by Unonbond =

∑ ∑ UPP + ∑ ∑ US S i j

i

+

i j

j